illumina / isaac4 Goto Github PK
View Code? Open in Web Editor NEWIsaac aligner version 4
License: Other
isaac4's People
Stargazers
Watchers
isaac4's Issues
Question about --use-smith-waterman option
Hello,
I am glad to post about using the isaac4 aligner.
I am wondering that Isaac aligner --use-smith-waterman smart option.
--use-smith-waterman arg (=smart)
One of the following:
- always : Use smith-waterman to reduce the amount of mismatches in aligned reads
- smart : apply heuristics to avoid executing costly smith-waterman on sequences that are unlikely to produce gaps
- never : Don't use smith-waterman
According to the isaac aligner tool description (https://github.com/Illumina/Isaac4/blob/master/src/markdown/manual.md), when we used the smart option, the mapping position is found by the heuristic method. but if I use the heuristic method, does all the seed length I specified are used for analysis although read doesn't have a gap?
- I want to know although some reads didn't have a gap, the Isaac aligner uses all of the seed lengths for alignment.
- If we use the "--use-smith-waterman no" option, does the analysis not use the seed length we specified?
New AMD Server AMD EPYC 7532 configure errors with CMAKE_HAVE_LIBC_PTHREAD and errors with make
Hi Roman,
new servers on Centos 8.4. Supports NUMA and has sse4_2
Configure finishes but there are error in CMakeError.log. Running make starts but dies with errors like c++/include/bgzf/BgzfReader.hh:98:19: error: expected ‘;’ at end of member declaration lower below you have the outputs of CMakeError.log and the output of make.
I tried different versions of gcc (10.3 and 9.3 and 8.4.0) and my own version of boost (which Isaac still doesn't like)... and the outcome is always the same. Do I have to go with and older version of gcc ? Would the PThread errors in configure cause the BgzfReader errors ?
Any clues ? Pointers ?
Thanks,
B
Command line for confgure:
../Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/configure --parallel=6 --verbose --with-numa --with-avx2 --prefix=/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19-bin
Configure finishes:
[SNIP]
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
[SNIP]
-- using compiler: gcc version 9.3.0
-- Found ccache: /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/ccache
-- Adding the c++ library subdirectory: bgzf
-- Adding the c++ library subdirectory: common
-- Adding the c++ library subdirectory: oligo
-- Adding the c++ library subdirectory: io
-- Adding the c++ library subdirectory: rta
-- Adding the c++ library subdirectory: flowcell
-- Adding the c++ library subdirectory: demultiplexing
-- Adding the c++ library subdirectory: xml
-- Adding the c++ library subdirectory: reference
-- Adding the c++ library subdirectory: bam
-- Adding the c++ library subdirectory: options
-- Adding the c++ library subdirectory: statistics
-- Adding the c++ library subdirectory: alignment
-- Adding the c++ library subdirectory: build
-- Adding the c++ library subdirectory: package
-- Adding the c++ library subdirectory: reports
-- Adding the c++ library subdirectory: workflow
-- Adding the c++ program subdirectory: bin
-- Adding the c++ program subdirectory: libexec
-- Found Doxygen: /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/doxygen (found version "1.8.16") found components: doxygen dot
-- Doxygen: /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/doxygen. Dot: /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/dot.
-- Creating Doxygen config file: /home/bfiset/lw-project/Isaac_Build/c++/Doxyfile
-- Could NOT find Markdown (missing: MARKDOWN_EXECUTABLE)
-- Markdown: MARKDOWN_EXECUTABLE-NOTFOUND.
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
iSAAC_DOCDIR
iSAAC_INCLUDEDIR
iSAAC_MANDIR
-- Build files have been written to: /home/bfiset/lw-project/Isaac_Build
The build directory /home/bfiset/lw-project/Isaac_Build was configured successfully
Type make at the top level of the root directory to build Isaac
But these errors in CMakeFiles/CMakeError.log
Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
Run Build Command(s):/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/gmake cmTC_50487/fast && /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/gmake -f CMakeFiles/cmTC_50487.dir/build.make CMakeFiles/cmTC_50487.dir/build
gmake[1]: Entering directory '/project/6014302/bfiset/Isaac_Build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_50487.dir/src.c.o
/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin/gcc -DCMAKE_HAVE_LIBC_PTHREAD -o CMakeFiles/cmTC_50487.dir/src.c.o -c /home/bfiset/lw-project/Isaac_Build/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_50487
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_50487.dir/link.txt --verbose=1
/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin/gcc -DCMAKE_HAVE_LIBC_PTHREAD -rdynamic CMakeFiles/cmTC_50487.dir/src.c.o -o cmTC_50487
CMakeFiles/cmTC_50487.dir/src.c.o:src.c:function main: error: undefined reference to 'pthread_create'
CMakeFiles/cmTC_50487.dir/src.c.o:src.c:function main: error: undefined reference to 'pthread_detach'
CMakeFiles/cmTC_50487.dir/src.c.o:src.c:function main: error: undefined reference to 'pthread_join'
collect2: error: ld returned 1 exit status
gmake[1]: *** [CMakeFiles/cmTC_50487.dir/build.make:87: cmTC_50487] Error 1
gmake[1]: Leaving directory '/project/6014302/bfiset/Isaac_Build/CMakeFiles/CMakeTmp'
gmake: *** [Makefile:121: cmTC_50487/fast] Error 2
Source file was:
#include <pthread.h>
void* test_func(void* data)
{
return data;
}
int main(void)
{
pthread_t thread;
pthread_create(&thread, NULL, test_func, NULL);
pthread_detach(thread);
pthread_join(thread, NULL);
pthread_atfork(NULL, NULL, NULL);
pthread_exit(NULL);
return 0;
}
Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/bfiset/lw-project/Isaac_Build/CMakeFiles/CMakeTmp
Run Build Command(s):/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/gmake cmTC_7ec55/fast && /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/gmake -f CMakeFiles/cmTC_7ec55.dir/build.make CMakeFiles/cmTC_7ec55.dir/build
gmake[1]: Entering directory '/project/6014302/bfiset/Isaac_Build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_7ec55.dir/CheckFunctionExists.c.o
/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTC_7ec55.dir/CheckFunctionExists.c.o -c /cvmfs/soft.computecanada.ca/gentoo/2020/usr/share/cmake/M
odules/CheckFunctionExists.c
Linking C executable cmTC_7ec55
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_7ec55.dir/link.txt --verbose=1
/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create -rdynamic CMakeFiles/cmTC_7ec55.dir/CheckFunctionExists.c.o -o cmTC_7ec55 -lpthreads
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/x86_64-pc-linux-gnu/binutils-bin/2.33.1/ld.gold: error: cannot find -lpthreads
CMakeFiles/cmTC_7ec55.dir/CheckFunctionExists.c.o:CheckFunctionExists.c:function main: error: undefined reference to 'pthread_create'
collect2: error: ld returned 1 exit status
gmake[1]: *** [CMakeFiles/cmTC_7ec55.dir/build.make:87: cmTC_7ec55] Error 1
gmake[1]: Leaving directory '/project/6014302/bfiset/Isaac_Build/CMakeFiles/CMakeTmp'
gmake: *** [Makefile:121: cmTC_7ec55/fast] Error 2
Determining if the include file cppunit/config-auto.h exists failed with the following output:
Change Dir: /home/bfiset/lw-project/Isaac_Build/CMakeFiles/CMakeTmp
Run Build Command(s):/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/gmake cmTC_8ea56/fast && /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/gmake -f CMakeFiles/cmTC_8ea56.dir/build.make CMakeFiles/cmTC_8ea56.dir/build
gmake[1]: Entering directory '/project/6014302/bfiset/Isaac_Build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_8ea56.dir/CheckIncludeFile.c.o
/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin/gcc -o CMakeFiles/cmTC_8ea56.dir/CheckIncludeFile.c.o -c /home/bfiset/lw-project/Isaac_Build/CMakeFiles/CMakeTmp/CheckIncludeFile.c
/home/bfiset/lw-project/Isaac_Build/CMakeFiles/CMakeTmp/CheckIncludeFile.c:1:10: fatal error: cppunit/config-auto.h: No such file or directory
1 | #include <cppunit/config-auto.h>
| ^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
gmake[1]: *** [CMakeFiles/cmTC_8ea56.dir/build.make:66: CMakeFiles/cmTC_8ea56.dir/CheckIncludeFile.c.o] Error 1
gmake[1]: Leaving directory '/project/6014302/bfiset/Isaac_Build/CMakeFiles/CMakeTmp'
gmake: *** [Makefile:121: cmTC_8ea56/fast] Error 2
And running make goes kaboom !!!
make
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/cmake -S/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src -B/home/bfiset/lw-project/Isaac_Build --check-build-system CMakeFiles/Makefile.cmake 0
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/cmake -E cmake_progress_start /home/bfiset/lw-project/Isaac_Build/CMakeFiles /home/bfiset/lw-project/Isaac_Build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/project/6014302/bfiset/Isaac_Build'
make -f CMakeFiles/iSAAC_OPT.dir/build.make CMakeFiles/iSAAC_OPT.dir/depend
make[2]: Entering directory '/project/6014302/bfiset/Isaac_Build'
cd /home/bfiset/lw-project/Isaac_Build && /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src /home/bfiset/lw-project/Isaac_Build /home/bfiset/lw-project/Isaac_Build /home/bfiset/lw-project/Isaac_Build/CMakeFiles/iSAAC_OPT.dir/DependInfo.cmake --color=
Scanning dependencies of target iSAAC_OPT
make[2]: Leaving directory '/project/6014302/bfiset/Isaac_Build'
make -f CMakeFiles/iSAAC_OPT.dir/build.make CMakeFiles/iSAAC_OPT.dir/build
make[2]: Entering directory '/project/6014302/bfiset/Isaac_Build'
make[2]: Nothing to be done for 'CMakeFiles/iSAAC_OPT.dir/build'.
make[2]: Leaving directory '/project/6014302/bfiset/Isaac_Build'
[ 0%] Built target iSAAC_OPT
make -f c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/build.make c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/depend
make[2]: Entering directory '/project/6014302/bfiset/Isaac_Build'
cd /home/bfiset/lw-project/Isaac_Build && /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/lib/bgzf /home/bfiset/lw-project/Isaac_Build /home/bfiset/lw-project/Isaac_Build/c++/lib/bgzf /home/bfiset/lw-project/Isaac_Build/c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/DependInfo.cmake --color=
Scanning dependencies of target isaac_bgzf
make[2]: Leaving directory '/project/6014302/bfiset/Isaac_Build'
make -f c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/build.make c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/build
make[2]: Entering directory '/project/6014302/bfiset/Isaac_Build'
[ 1%] Building CXX object c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/BgzfReader.cpp.o
cd /home/bfiset/lw-project/Isaac_Build/c++/lib/bgzf && /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/ccache /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin/g++ -I/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include -I/home/bfiset/lw-project/Isaac_Build/c++ -I/home/bfiset/lw-project/Isaac_Build/c++/lib/bgzf -I/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/lib/bgzf -I/home/bfiset/lw-project/Isaac_Build/c++/common -isystem /cvmfs/soft.computecanada.ca/gentoo/2020/usr/include/libxml2 -isystem /home/bfiset/lw-project/Isaac_Build/bootstrap/include -std=gnu++0x -fpermissive -fopenmp -Wall -Wextra -Wunused -Wno-long-long -Wsign-compare -Wpointer-arith -Wno-unused-local-typedefs -Wno-deprecated-declarations -DBOOST_SYSTEM_API_CONFIG_HPP -DBOOST_POSIX_API -Wno-unused-parameter -mavx2 -O2 -ftree-vectorize -finline-functions -fpredictive-commoning -fgcse-after-reload -funswitch-loops -ftree-slp-vectorize -fvect-cost-model -fipa-cp-clone -ftree-phiprop -ggdb -o CMakeFiles/isaac_bgzf.dir/BgzfReader.cpp.o -c /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/lib/bgzf/BgzfReader.cpp
In file included from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/lib/bgzf/BgzfReader.cpp:25:
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:98:19: error: expected ‘;’ at end of member declaration
98 | static voidpf zalloc OF((voidpf opaque, uInt items, uInt size))
| ^~~~~~
| ;
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:98:29: error: expected identifier before ‘(’ token
98 | static voidpf zalloc OF((voidpf opaque, uInt items, uInt size))
| ^
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:98:67: warning: ISO C++ forbids declaration of ‘OF’ with no type [-fpermissive]
98 | static voidpf zalloc OF((voidpf opaque, uInt items, uInt size))
| ^
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:105:17: error: variable or field ‘zfree’ declared void
105 | static void zfree OF((voidpf opaque, voidpf address))
| ^~~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:105:17: error: expected ‘;’ at end of member declaration
105 | static void zfree OF((voidpf opaque, voidpf address))
| ^~~~~
| ;
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:105:26: error: expected identifier before ‘(’ token
105 | static void zfree OF((voidpf opaque, voidpf address))
| ^
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:105:57: warning: ISO C++ forbids declaration of ‘OF’ with no type [-fpermissive]
105 | static void zfree OF((voidpf opaque, voidpf address))
| ^
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh: In member function ‘void isaac::bgzf::BgzfReader::reset()’:
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:87:24: warning: invalid conversion from ‘voidpf’ {aka ‘void*’} to ‘alloc_func’ {aka ‘void* (*)(void*, unsigned int, unsigned int)’} [-fpermissive]
87 | strm_.zalloc = zalloc;
| ^~~~~~
| |
| voidpf {aka void*}
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:88:23: error: ‘zfree’ was not declared in this scope; did you mean ‘free’?
88 | strm_.zfree = zfree;
| ^~~~~
| free
In file included from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/common/Threads.hpp:26,
from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:29,
from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/lib/bgzf/BgzfReader.cpp:25:
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh: In member function ‘int isaac::bgzf::BgzfReader::OF(int (*)(voidpf, uInt, uInt))’:
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:100:56: error: ‘opaque’ was not declared in this scope
100 | ISAAC_ASSERT_MSG(reinterpret_cast<BgzfReader*>(opaque)->zalbufferFree, "Unexpected too many zalloc calls");
| ^~~~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/common/Debug.hh:77:42: note: in definition of macro ‘ISAAC_ASSERT_MSG’
77 | #define ISAAC_ASSERT_MSG(expr, msg) {if (expr) {} else \
| ^~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:101:63: error: ‘opaque’ was not declared in this scope
101 | ISAAC_ASSERT_MSG(sizeof(reinterpret_cast<BgzfReader*>(opaque)->zalbuffer[reinterpret_cast<BgzfReader*>(opaque)->zalbufferFree]) >= items * size, "Unexpected buffer size passed to zalloc : size=" << size << " items=" << items);
| ^~~~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/common/Debug.hh:77:42: note: in definition of macro ‘ISAAC_ASSERT_MSG’
77 | #define ISAAC_ASSERT_MSG(expr, msg) {if (expr) {} else \
| ^~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:101:140: error: ‘items’ was not declared in this scope
101 | ISAAC_ASSERT_MSG(sizeof(reinterpret_cast<BgzfReader*>(opaque)->zalbuffer[reinterpret_cast<BgzfReader*>(opaque)->zalbufferFree]) >= items * size, "Unexpected buffer size passed to zalloc : size=" << size << " items=" << items);
| ^~~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/common/Debug.hh:77:42: note: in definition of macro ‘ISAAC_ASSERT_MSG’
77 | #define ISAAC_ASSERT_MSG(expr, msg) {if (expr) {} else \
| ^~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:101:148: error: ‘size’ was not declared in this scope
101 | ISAAC_ASSERT_MSG(sizeof(reinterpret_cast<BgzfReader*>(opaque)->zalbuffer[reinterpret_cast<BgzfReader*>(opaque)->zalbufferFree]) >= items * size, "Unexpected buffer size passed to zalloc : size=" << size << " items=" << items);
| ^~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/common/Debug.hh:77:42: note: in definition of macro ‘ISAAC_ASSERT_MSG’
77 | #define ISAAC_ASSERT_MSG(expr, msg) {if (expr) {} else \
| ^~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:101:148: note: suggested alternatives:
101 | ISAAC_ASSERT_MSG(sizeof(reinterpret_cast<BgzfReader*>(opaque)->zalbuffer[reinterpret_cast<BgzfReader*>(opaque)->zalbufferFree]) >= items * size, "Unexpected buffer size passed to zalloc : size=" << size << " items=" << items);
| ^~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/common/Debug.hh:77:42: note: in definition of macro ‘ISAAC_ASSERT_MSG’
77 | #define ISAAC_ASSERT_MSG(expr, msg) {if (expr) {} else \
| ^~~~
In file included from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/range/functions.hpp:20,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/range/iterator_range_core.hpp:38,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/range/iterator_range.hpp:13,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/iostreams/traits.hpp:38,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/iostreams/pipeline.hpp:18,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/iostreams/detail/push.hpp:22,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/iostreams/filtering_stream.hpp:19,
from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/lib/bgzf/BgzfReader.cpp:21:
/home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/range/size.hpp:55:5: note: ‘boost::size’
55 | size(const SinglePassRange& rng)
| ^~~~
In file included from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/mpl/vector/aux_/size.hpp:17,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/mpl/vector/vector0.hpp:26,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/mpl/vector/vector10.hpp:18,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/mpl/vector/vector20.hpp:18,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/numeric/ublas/detail/returntype_deduction.hpp:13,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/numeric/ublas/traits.hpp:22,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/numeric/ublas/storage.hpp:26,
from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/../common/StaticVector.hh:24,
from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:27,
from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/lib/bgzf/BgzfReader.cpp:25:
/home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/mpl/size_fwd.hpp:20:38: note: ‘boost::mpl::size’
20 | template< typename Sequence > struct size;
| ^~~~
In file included from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/numeric/ublas/detail/config.hpp:300,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/numeric/ublas/exception.hpp:19,
from /home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/numeric/ublas/storage.hpp:25,
from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/../common/StaticVector.hh:24,
from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:27,
from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/lib/bgzf/BgzfReader.cpp:25:
/home/bfiset/lw-project/Isaac_Build/bootstrap/include/boost/numeric/ublas/detail/definitions.hpp:177:31: note: ‘boost::numeric::ublas::dimension::size’
177 | typename E::size_type size (const E& e) {
| ^~~~
In file included from /home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/lib/bgzf/BgzfReader.cpp:25:
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:102:41: error: ‘opaque’ was not declared in this scope
102 | --reinterpret_cast<BgzfReader*>(opaque)->zalbufferFree;
| ^~~~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh: In member function ‘int isaac::bgzf::BgzfReader::OF(int (*)(voidpf, voidpf))’:
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:109:41: error: ‘opaque’ was not declared in this scope
109 | ++reinterpret_cast<BgzfReader*>(opaque)->zalbufferFree;
| ^~~~~~
/home/bfiset/lw-project/Isaac4-Build-Isaac-04.20.06.19/Isaac4-master/src/c++/include/bgzf/BgzfReader.hh:110:5: warning: no return statement in function returning non-void [-Wreturn-type]
110 | }
| ^
make[2]: *** [c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/build.make:66: c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/BgzfReader.cpp.o] Error 1
make[2]: Leaving directory '/project/6014302/bfiset/Isaac_Build'
make[1]: *** [CMakeFiles/Makefile2:845: c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/all] Error 2
make[1]: Leaving directory '/project/6014302/bfiset/Isaac_Build'
make: *** [Makefile:144: all] Error 2
Questions about how to use this aligner
1) For the alignment of the human whole exome sequence FASTA data to the human GRCh38p14 reference genome, and using the Isaac aligner V4, do you recommend:
- unmasked genome reference ?
- masked genome reference ?
- reference with hs38d1 decoy sequence included ?
2) Please define how the human reference genome sequences are masked for best use with Isaac aligner V4 and human exome FASTA alignment ?
- is it a soft mask ?
- is it a hard mask ?
3) For the alignment of the human whole genome sequence FASTA data to the human GRCh38p14 reference genome, and using the Isaac aligner V4, do you recommend:
- unmasked genome reference ?
- masked genome reference ?
- reference with hs38d1 decoy sequence included ?
4) To mark and remove PCR duplicates from the BAM file generated from either human exome or human whole genome FASTA, what parameters are set with Isaac aligner V4:
Option 1:
--keep-duplicates 1 or --keep-duplicates 0
OR
Option 2:
--mark-duplicates 1 or --mark-duplicates 0
LD error in installation
I'm trying to install Isaac4 on an Ubuntu based workstation (Pop_OS! 20.10 with all dependencies installed) and am coming across a compilation error at the make step.
The relevant error in the output trace is:
[ 97%] Linking CXX executable isaac-align
/usr/bin/ld: /usr/bin/ld: DWARF error: could not find variable specification at offset 805b4
/usr/bin/ld: DWARF error: could not find variable specification at offset 805d6
../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function `void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<20u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<20u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/home/bubbz/Downloads/Isaac4/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to `void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<20u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<20u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
/usr/bin/ld: ../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function `void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<19u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<19u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/home/bubbz/Downloads/Isaac4/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to `void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<19u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<19u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
/usr/bin/ld: ../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function `void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<18u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<18u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/home/bubbz/Downloads/Isaac4/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to `void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<18u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<18u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
/usr/bin/ld: ../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function `void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<17u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<17u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/home/bubbz/Downloads/Isaac4/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to `void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<17u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<17u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
/usr/bin/ld: ../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function `void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<16u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<16u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/home/bubbz/Downloads/Isaac4/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to `void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<16u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<16u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
/usr/bin/ld: ../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function `void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<15u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<15u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/home/bubbz/Downloads/Isaac4/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to `void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<15u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<15u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
/usr/bin/ld: ../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function `void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<14u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<14u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/home/bubbz/Downloads/Isaac4/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to `void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<14u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<14u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
/usr/bin/ld: ../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function `void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<13u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<13u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/home/bubbz/Downloads/Isaac4/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to `void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<13u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<13u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
/usr/bin/ld: ../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function `void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<12u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<12u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/home/bubbz/Downloads/Isaac4/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to `void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<12u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<12u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
/usr/bin/ld: ../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function `void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<11u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<11u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/home/bubbz/Downloads/Isaac4/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to `void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<11u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<11u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
/usr/bin/ld: ../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function `void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<10u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<10u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/home/bubbz/Downloads/Isaac4/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to `void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<10u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<10u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
collect2: error: ld returned 1 exit status
make[2]: *** [c++/bin/CMakeFiles/isaac-align.dir/build.make:124: c++/bin/isaac-align] Error 1
make[2]: Leaving directory '/home/bubbz/Downloads/Isaac-build'
make[1]: *** [CMakeFiles/Makefile2:1339: c++/bin/CMakeFiles/isaac-align.dir/all] Error 2
make[1]: Leaving directory '/home/bubbz/Downloads/Isaac-build'
make: *** [Makefile:139: all] Error 2
I have re-cloned the repo a coupled of times to ensure that the files where transfered from GitHub as expected but the same error is cropping up. Let me know if there are any corrections that need to be made to allow the software to compile or any additonal information that you would need to troubleshoot this issue,
Thanks,
Matt
installation error
Hi,
I was trying to install Isaac4 after git clone, but encountered error with "make" step:
Isaac4/Isaac-build>make
[ 0%] Built target iSAAC_OPT
[ 1%] Building CXX object c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/BgzfReader.cpp.o
In file included from ./Isaac4/src/c++/include/bgzf/BgzfReader.hh:29:0,
from ./Isaac4/src/c++/lib/bgzf/BgzfReader.cpp:25:
./Isaac4/src/c++/include/common/Threads.hpp: In destructor 'isaac::common::BasicThreadVector::~BasicThreadVector()':
./Isaac4/src/c++/include/common/Threads.hpp:198:73: error: '_1' was not declared in this scope
std::for_each(begin(), end(), boost::bind(&boost::thread::join, _1));
^
'''''''
BOOST_STATIC_CONSTEXPR boost::arg<1> 1;
^
In file included from /netopt/tools64/boost-1.76.0-ncbi1/include/boost-1_76/boost/mpl/aux/include_preprocessed.hpp:37:0,
from /netopt/tools64/boost-1.76.0-ncbi1/include/boost-1_76/boost/mpl/placeholders.hpp:43,
from /netopt/tools64/boost-1.76.0-ncbi1/include/boost-1_76/boost/iterator/iterator_categories.hpp:16,
from /netopt/tools64/boost-1.76.0-ncbi1/include/boost-1_76/boost/iterator/iterator_facade.hpp:13,
from /netopt/tools64/boost-1.76.0-ncbi1/include/boost-1_76/boost/range/iterator_range_core.hpp:27,
from /netopt/tools64/boost-1.76.0-ncbi1/include/boost-1_76/boost/range/iterator_range.hpp:13,
from /netopt/tools64/boost-1.76.0-ncbi1/include/boost-1_76/boost/iostreams/traits.hpp:38,
from /netopt/tools64/boost-1.76.0-ncbi1/include/boost-1_76/boost/iostreams/pipeline.hpp:18,
from /netopt/tools64/boost-1.76.0-ncbi1/include/boost-1_76/boost/iostreams/detail/push.hpp:22,
from /netopt/tools64/boost-1.76.0-ncbi1/include/boost-1_76/boost/iostreams/filtering_stream.hpp:19,
from ./Isaac4/src/c++/lib/bgzf/BgzfReader.cpp:21:
/netopt/tools64/boost-1.76.0-ncbi1/include/boost-1_76/boost/mpl/aux_/preprocessed/gcc/placeholders.hpp:29:16: note: 'mpl_::_1'
typedef arg<1> _1;
^
make[2]: *** [c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/BgzfReader.cpp.o] Error 1
make[1]: *** [c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/all] Error 2
make: *** [all] Error 2
Any help or suggestion is appreciated
comparing two samples in terms of mapping qualities
This is not an issue but rather asking for advice.
I have two cohorts A and B. Variant calls from A and B are very different in terms of quality. I couldnt find anything on variant calling so i want to compare mapped files (bams).
In the simplest way.
both cohorts have their data on bam forma(mapped on hg19 with bwa).
So I am proccesing them as follows.
bam --> (samtools sort -n | samtools fastq) --> Isaac4 --> StrelkaSomaticVariant Calling.
isaac-align -r sorted-reference.xml -b fastq-dir -o output -t temp-space-path --base-calls-format fastq-gz -m 700 -j62 --verbosity 0
2019-05-29 11:07:51 [7f16d4d4b7c0] Forcing LC_ALL to C
2019-05-29 11:07:51 [7f16d4d4b7c0] Version: Isaac-04.17.06.15
2019-05-29 11:07:51 [7f16d4d4b7c0] argc: 2 argv: ./isaac-align -v
Isaac-04.17.06.15
So my questions,
- What should be my measure of comparison? I will definetely read the mapping scoring in detailed but I see lots of MAPQ0 in the sam. Is there an another measure from Isaac that I can use it?
Thank you for your help and time,
Best regards,
Tunc
about version 04.17.06.15
Hi,
We are investigating multiple WGS tumor samples. From three projects we have three different pipelines. To be able to compare apples and apples, could you help me to find Isaac aligner version 04.17.06.15. It was used in project that we cannot realy have the fastqs. So that we have to map the remaining samples with this version to make unbiased comparison.
Thank you very much for the help,
Best regards,
Tunc.
ISAAC4 throws exceptions in fastqs with reads of different length
I am applying ISAAC4 to fastq files which contain reads of different lengths (the sequence length and quality string length still match).
There are several valid reasons why reads within a FASTQ would have different lengths (for example read trimming). Should I not be encountering this error or is this an expected behavior for ISAAC4? Would support for reads of different lengths within a file be a supported use case in the future?
Trying Issac Example and get core dumped
Hi,
Finally have gotten Issac to compile and trying the included example before trying production and get this on one system:
./isaac-align -r ./examples/PhiX/iGenomes/PhiX/NCBI/1993-04-28/Sequence/Chromosomes/phix.fa -b ./examples/PhiX/Fastq -f fastq --use-bases-mask y150,y150 -m40
2018-01-31 17:10:46 [2b33e38ef2c0] Forcing LC_ALL to C
2018-01-31 17:10:46 [2b33e38ef2c0] Version: Isaac-04.18.01.19
2018-01-31 17:10:46 [2b33e38ef2c0] argc: 10 argv: ./isaac-align -r ./examples/PhiX/iGenomes/PhiX/NCBI/1993-04-28/Sequence/Chromosomes/phix.fa -b ./examples/PhiX/Fastq -f fastq --use-bases-mask y150,y150 -m40
2018-01-31 17:10:46 [2b33e38ef2c0] FastqReader uncompressedBufferSize_=67108864
2018-01-31 17:11:05 [2b33e38ef2c0] Opened fastq stream on /mnt/parallel_scratch_mp2_wipe_on_december_2018/pfiset1/bfiset/Isaac-V4/./examples/PhiX/Fastq/lane1_read1.fastq and base Q0 !
2018-01-31 17:11:05 [2b33e38ef2c0] FastqReader uncompressedBufferSize_=67108864
2018-01-31 17:11:14 [2b33e38ef2c0] Opened fastq stream on /mnt/parallel_scratch_mp2_wipe_on_december_2018/pfiset1/bfiset/Isaac-V4/./examples/PhiX/Fastq/lane1_read2.fastq and base Q0 !
2018-01-31 17:11:14 [2b33e38ef2c0] FastqFlowcellInfo(XXXXXXXXX,99:35,[1 ],48nl,)
Illegal instruction (core dumped)
Any hints ?
Thanks,
B.
internal program error?
Hi,
Could you help me to fix the following error. Interestingly, out of ~30 samples only one of raised the error.
I am runnning isaac with 62 cores and 700 gb memory. We are mapping human samples.
Thank you very much for your help,
Tunc.
2019-03-18 13:38:46 [7feeb8fa4700] ERROR: ***** Internal Program Error - assertion (end_ != current_) failed in isaac::oligo::KmerGenerator<kmerLength, T, InputIteratorT, step, TranslatorT>::KmerGenerator(InputIteratorT, InputIteratorT, const TranslatorT&) [with unsigned int kmerLength = 8u; T = unsigned int; InputIteratorT = __gnu_cxx::__normal_iterator<const char*, std::vector<char, isaac::common::NumaAllocator<char, 0> > >; unsigned int step = 1u; TranslatorT = isaac::oligo::Translator<>]:/groups/lackgrp/ICGC-Prostate/Reference-Files/Isaac_African_Project/Isaac4/src/c++/include/oligo/KmerGenerator.hpp(62): Empty sequence not supported
/usr/bin/bash: line 1: 237418 Segmentation fault /groups/lackgrp/ICGC-Prostate/Reference-Files/Isaac_African_Project/Isaac4/isaac-build/bin/isaac-align -r /groups/lackgrp/ICGC-Prostate/Reference-Files/Isaac_Reference/sorted-reference.xml -b analysis/CH40/temp-DNA.CH40N.remDup_Realigned_Recal.Merged.remDup_T-B_realigned -o analysis/CH40/AlingmentIsaac-DNA.CH40N.remDup_Realigned_Recal.Merged.remDup_T-B_realigned -t analysis/CH40/Isaac_Intermediate-DNA.CH40N.remDup_Realigned_Recal.Merged.remDup_T-B_realigned --base-calls-format fastq-gz -m 700 -j62 --verbosity 0
[Mon Mar 18 13:38:46 2019]
Error in rule mapping_isaac4:
jobid: 0
output: analysis/CH40/GRCh38-DNA.CH40N.remDup_Realigned_Recal.Merged.remDup_T-B_realigned.bam
GIFs are not generated
Hi Roman,
I can't get the GIF to be generated for the reports even with gnuplot loaded... tried 4.6 and 5.1 using the option --stats-image-format gif.
Any tips ?
Thanks
Problem with installation on ubuntu 19.10
I get the following error when trying to install:
[ 49%] Building CXX object c++/lib/alignment/CMakeFiles/isaac_alignment.dir/TemplateBuilder.cpp.o
/home/chriad/Desktop/nebula/isaac/Isaac4/src/c++/lib/alignment/TemplateBuilder.cpp: In constructor ‘isaac::alignment::TemplateBuilder::TemplateBuilder(bool, const FlowcellLayoutList&, std::size_t, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, bool, bool, bool, bool, unsigned int, unsigned int, bool, unsigned int, bool, const isaac::alignment::AlignmentCfg&, isaac::alignment::TemplateBuilder::DodgyAlignmentScore, unsigned int, bool)’:
/home/chriad/Desktop/nebula/isaac/Isaac4/src/c++/lib/alignment/TemplateBuilder.cpp:74:30: error: ‘pow10’ was not declared in this scope
74 | , anomalousPairHandicap_(pow10(double(anomalousPairHandicap) / 10.0) - 1.0)//anomalousPairHandicap)
| ^~~~~
make[2]: *** [c++/lib/alignment/CMakeFiles/isaac_alignment.dir/build.make:206: c++/lib/alignment/CMakeFiles/isaac_alignment.dir/TemplateBuilder.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:998: c++/lib/alignment/CMakeFiles/isaac_alignment.dir/all] Error 2
Does it have to do with the version of glibc? (see https://abi-laboratory.pro/?view=changelog&l=glibc&v=2.27)
- The libm functions pow10, pow10f and pow10l are no longer supported for
new programs. Programs should use the standard names exp10, exp10f and
exp10l for these functions instead.
I use version 2.30
$ /lib/x86_64-linux-gnu/libc.so.6 --version
GNU C Library (Ubuntu GLIBC 2.30-0ubuntu2.1) stable release version 2.30.
What can I do to get it running?
Installation Error
While installing Isaac4 I encountered the following error:
~/Isaac4/src/c++/lib/common/SystemCompatibility.cpp: In function ‘void* isaac::common::malloc_hook(size_t, const void*)’:
~/Isaac4/src/c++/lib/common/SystemCompatibility.cpp:464:5: error: ‘__malloc_hook’ was not declared in this scope; did you mean ‘malloc_hook’?
464 | __malloc_hook = old_malloc_hook_;
| ^~~~~~~~~~~~~
| malloc_hook
In file included from /usr/include/c++/11/cassert:44,
from ~/Isaac4/src/c++/lib/common/SystemCompatibility.cpp:74:
~/Isaac4/src/c++/lib/common/SystemCompatibility.cpp: In function ‘void isaac::common::hookMalloc(bool (*)(size_t, const void*))’:
~/Isaac4/src/c++/lib/common/SystemCompatibility.cpp:487:12: error: ‘__malloc_hook’ was not declared in this scope; did you mean ‘malloc_hook’?
487 | assert(__malloc_hook != malloc_hook);
| ^~~~~~~~~~~~~
~/Isaac4/src/c++/lib/common/SystemCompatibility.cpp: In function ‘unsigned int isaac::common::unhookMalloc(bool (*)(size_t, const void*))’:
~/Isaac4/src/c++/lib/common/SystemCompatibility.cpp:501:12: error: ‘__malloc_hook’ was not declared in this scope; did you mean ‘malloc_hook’?
501 | assert(__malloc_hook == malloc_hook);
| ^~~~~~~~~~~~~Please let me know if you need further details to reproduce the error.
ISaac install error
when i install the up-to-date Isaac4，i have meet a problem.
[ 40%] Building C object Utilities/cmlibarchive/libarchive/CMakeFiles/cmlibarchive.dir/archive_cryptor.c.o In file included from /home/software/Isaac42/Isaac-build/bootstrap_cmake/build/cmake-3.7.0-rc2/Utilities/cmlibarchive/libarchive/archive_cryptor.c:32:0: /home/software/Isaac42/Isaac-build/bootstrap_cmake/build/cmake-3.7.0-rc2/Utilities/cmlibarchive/libarchive/archive_cryptor_private.h:107:17: error: field ‘ctx’ has incomplete type EVP_CIPHER_CTX ctx;
I have search the error in google, some one think i should change openssl version. when i change the version to 1.1.0g. the software still can't install.
so, how can i solve the problem?
Isaac can't configure project
Dear all,
I'm trying to build the project by following the instruction listed in src/INSTALL. Here are some details regarding my attempt (Boost 1.66,
[asabaini@node001 Isaac-build]$ gcc --version
gcc (GCC) 6.3.0
Copyright (C) 2016 Free Software Foundation, Inc.
[asabaini@node001 Isaac-build]$ cmake --version
cmake version 3.11.0
[asabaini@node001 Isaac-build]$ ccache --version
ccache version 3.4.2
[asabaini@node001 Isaac-build]$ ../src/configure --prefix=/cm/shared/apps/isaac/4 --with-cmake=$(which cmake) --build-type=MinSizeRel --without-numa --without-unit-tests
Salient parts of the log are
...
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
...
-- Could NOT find LibXml2: Found unsuitable version "2.9.1", but required is at least "2.9.6" (found /usr/lib64/libxml2.so)
-- Could NOT find LibXslt: Found unsuitable version "1.1.28", but required is at least "1.1.31" (found /usr/lib/libxslt.so)
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1")
-- Checking for module 'libexslt'
-- No package 'libexslt' found
-- Found LibExslt: /usr/lib/libexslt.so (Required is at least version "0.8.19")
...
-- Successfuly unpacked /local/Isaac4-Isaac-04.18.01.19/src/../redist/libxml2-2.9.6.tar.gz from the distribution package...
configuring LIBXML2
-- Successfuly configured libxml2-2.9.6 from the distribution package...
installing LIBXML2
-- Successfuly built libxml2-2.9.6 from the distribution package...
-- Find library redist , HINTS /local/Isaac4-Isaac-04.18.01.19/Isaac-build/bootstrap/lib: /usr/lib64/libxml2.so
-- Found redist LIBXML2 header: /local/Isaac4-Isaac-04.18.01.19/Isaac-build/bootstrap/include/libxml2/libxml/xpath.h
-- Found redist LIBXML2 library: /usr/lib64/libxml2.so
unpacking (/local/Isaac4-Isaac-04.18.01.19/src/../redist/libxslt-1.1.31.tar.gz)
-- Successfuly unpacked /local/Isaac4-Isaac-04.18.01.19/src/../redist/libxslt-1.1.31.tar.gz from the distribution package...
configuring LIBXSLT
-- Successfuly configured libxslt-1.1.31 from the distribution package...
installing LIBXSLT
...
-- Configuring incomplete, errors occurred!
See also "/local/Isaac4-Isaac-04.18.01.19/Isaac-build/CMakeFiles/CMakeOutput.log".
See also "/local/Isaac4-Isaac-04.18.01.19/Isaac-build/CMakeFiles/CMakeError.log".
Couldn't configure the project:
Attached you can find the complete logs. I can't really see what error is causing this issue. Can you please help me?
CMakeError.log
CMakeOutput.log
Thank you in advance
Alberto
isacc4 install error
my dear:
when I have already download the newest Isaac4:
/mnt/ilustre/centos7users/dna/.env/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/alignment/libisaac_alignment.a(MatchSelector.cpp.o): in function void isaac::alignment::MatchSelector::parallelSelect<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<20u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::alignment::matchFinder::TileClusterInfo&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocatorisaac::alignment::TemplateLengthStatistics >&, isaac::flowcell::TileMetadata const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<20u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, isaac::alignment::matchSelector::FragmentStorage&)':
/mnt/ilustre/centos7users/dna/biosoft/Isaac4-master/src/c++/lib/alignment/MatchSelector.cpp:333: undefined reference to void isaac::alignment::matchSelector::TemplateDetector::determineTemplateLengths<isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<20u>, isaac::common::NumaAllocator<void, -2> >, 4u> >(isaac::flowcell::TileMetadata const&, std::vector<isaac::alignment::matchFinder::ClusterInfo, std::allocator<isaac::alignment::matchFinder::ClusterInfo> > const&, std::vector<isaac::alignment::RestOfGenomeCorrection, std::allocator<isaac::alignment::RestOfGenomeCorrection> > const&, isaac::alignment::ClusterHashMatchFinder<isaac::reference::ReferenceHash<isaac::oligo::BasicKmerType<20u>, isaac::common::NumaAllocator<void, -2> >, 4u> const&, isaac::alignment::BasicBclClusters<isaac::common::NumaAllocator<char, -2> > const&, std::vector<isaac::alignment::TemplateLengthStatistics, std::allocator<isaac::alignment::TemplateLengthStatistics> >&, isaac::alignment::matchSelector::MatchSelectorStats&)'
How could I do? thankyou!
blocked allocation error of PE 300bp reads
Hi,
It seems isaac4 currently having issues with the mapping with PE 300bp fastq files. We tried it using the following command through both full-size fastq and 1000-reads fastq files:
isaac-align -r GCA_000001405.15_GRCh38.fa -b TEST1/ -f fastq --base-quality-cutoff 15 --default-adapters Standard --realign-gaps no --memory-control warning -m200 --jobs 4 --verbosity 4 -o TEST1run1
It always shows the following error
2023-08-10 17:55:48 [7f8525b71700] Resetting Fastq data for 8000000 clusters
2023-08-10 17:55:48 [7f8cc1322740] adding BarcodeMetadata(AACVWFKM5,1,default,none,(0), 0)
2023-08-10 17:55:48 [7f8cc1322740] STAT: FindHashMatchesTransition::processFlowcellTiles before findLaneMatches 54058553344vm 10447751res
2023-08-10 17:55:48 [7f8cc1322740] Resolving barcodes for Layout(AACVWFKM5, [,ReadMetadata(1, 300 [1, 300], 0id, 0off,1frc),ReadMetadata(2, 300 [302, 601], 1id, 300off,302frc)]) lane 1
2023-08-10 17:55:48 [7f8cc1322740] Forced barcode index for clusters of TileMetadata(AACVWFKM5, 1, 1, 1250, 0oi, 0) to BarcodeMetadata(AACVWFKM5,1,default,none,(0), 0)
2023-08-10 17:55:48 [7f8cc1322740] Resolving barcodes done for Layout(AACVWFKM5, [,ReadMetadata(1, 300 [1, 300], 0id, 0off,1frc),ReadMetadata(2, 300 [302, 601], 1id, 300off,302frc)]) lane 1
2023-08-10 17:55:48 [7f8cc1322740] Finding hash matches with repeat threshold: 100
2023-08-10 17:55:48 [7f8cc1322740] Allocating 4 tile stats.
2023-08-10 17:55:48 [7f8cc1322740] Allocating 4 tile stats done. Total size is 458880 bytes.
2023-08-10 17:55:48 [7f8cc1322740] Allocating 4 tile barcode stats.
2023-08-10 17:55:48 [7f8cc1322740] Allocating 4 tile barcode stats done. Total size is 1184 bytes.
2023-08-10 17:55:48 [7f8cc1322740] Resizing fragment storage for 1250 clusters
2023-08-10 17:55:48 [7f8cc1322740] Resizing fragment storage done for 1250 clusters
2023-08-10 17:55:48 [7f8cc1322740] Determining template length statistics for 1 barcodes on TileMetadata(AACVWFKM5, 1, 1, 1250, 0oi, 0)
Check failed in file /Isaac4-Isaac-04.18.01.19/bootstrap/include/boost/numeric/ublas/storage.hpp at line 364:
size <= N
2023-08-10 17:55:48 [7f8be5714700] WARNING: blocked allocation of 33 bytes requested.
2023-08-10 17:55:48 [7f8be5714700] WARNING: blocked allocation of 144 bytes requested.
2023-08-10 17:55:48 [7f8be5714700] WARNING: blocked allocation of 32 bytes requested.
terminate called after throwing an instance of 'boost::numeric::ublas::bad_size'
what(): bad size
Aborted (core dumped)
We are using a machine with 32 CPUs and 256GB RAM, any parameters we can adjust to make it work? Thank you in advance!
Running slower on more threads
Hi,
I've been testing Isaac's performance on different data sets, and I've been getting some mixed results. Namely, when using smaller data sets (below ~40GB), 36 CPU threads perform significantly better than 16 threads, while when using larger sets (>80 GB), 16 threads perform the task in half the time 36 threads do. I've tried adding the --jobs argument to the command line, but I didn't see much improvement.
Can you give me some advice on how to tackle this issue?
Thanks in advance,
Pavle
MARKDOWN_EXECUTABLE-NOTFOUND
As stated in the install file src/INSTALL
Prerequisites:
--------------
- markdown tool will be used if available to generate html user manual
So I'm guessing that if it is not available, nothing will be generated. I have no markdown tool installed, and I'm not interested in having html user manual. When I run configure, however, I get this error.
gcc --version
gcc (GCC) 6.3.0
cmake --version
cmake version 3.10.1
../src/configure --prefix=/apps/isaac/4 --with-cmake=$(which cmake) --build-type=MinSizeRel
...
-- Could NOT find Markdown (missing: MARKDOWN_EXECUTABLE)
-- Markdown: MARKDOWN_EXECUTABLE-NOTFOUND.
Is there a flag I'm missing for configure for disabling build markdown docs?
Failed to allocate a file handle
Hi,
I am testing isaac-align on one WGS sample and this is the command I used
/wynton/home/rotation/mtsui/ASE_project/Isaac4/bin/isaac-align \
-r ~/ASE_project/GRCh38.d1.vd1.fa \
-b $WES_DIR/$patient \
--base-calls-format fastq-gz \
-o $WES_DIR/$patient \
-t $TMPDIR \
-m 40
It appears to run fine and then I get a "Failed to allocate a file handle" error. I included the last lines of the error log here:
2022-01-20 13:31:01 [2b9b51e73cc0] STAT: ClusterHashMatchFinder::ClusterHashMatchFinder seedsPerMatch:2/4 6347304960vm 818531res
2022-01-20 13:31:01 [2b9b51e73cc0] STAT: before ClusterHashMatchFinder::ClusterHashMatchFinder seedsPerMatch:3/4 6347304960vm 818531res
2022-01-20 13:31:01 [2b9b51e73cc0] STAT: ClusterHashMatchFinder::ClusterHashMatchFinder seedsPerMatch:3/4 6348369920vm 818531res
2022-01-20 13:31:01 [2b9b51e73cc0] STAT: before ClusterHashMatchFinder::ClusterHashMatchFinder seedsPerMatch:4/4 6348369920vm 818531res
2022-01-20 13:31:01 [2b9b51e73cc0] STAT: ClusterHashMatchFinder::ClusterHashMatchFinder seedsPerMatch:4/4 6349172736vm 818531res
2022-01-20 13:31:01 [2b9b51e73cc0] STAT: TemplateBuilder before shadowList_.reserve 6360207360vm 818531res
2022-01-20 13:31:01 [2b9b51e73cc0] STAT: TemplateBuilder before bestCombinationPairInfo_.reserve 6361202688vm 818531res
2022-01-20 13:31:01 [2b9b51e73cc0] STAT: TemplateBuilder before bestRescuedPair_.reserve 6361202688vm 818597res
2022-01-20 13:31:01 [2b9b51e73cc0] STAT: TemplateBuilder before candidates_.reserve 6361202688vm 818597res
2022-01-20 13:31:01 [2b9b51e73cc0] STAT: TemplateBuilder after candidates_.reserve 6361452544vm 818597res
2022-01-20 13:31:01 [2b9b51e73cc0] STAT: Constructed match selector 6361452544vm 818597res
2022-01-20 13:31:11 [2b9b51e73cc0] STAT: Constructing ReferenceHasher: for 16-mers 24221159424vm 5023324res
2022-01-20 13:31:36 [2b9b51e73cc0] a:3308323 b:7048005 buckets:4294967296 and 2942474370 genome 16-mers unique k-mers found 954415372 unique keys. maxUniqueKeys:954415372
2022-01-20 13:31:42 [2b9b51e73cc0] STAT: reserving memory done for 2942474370 positions 35991060480vm 8052378res
2022-01-20 13:32:04 [2b9b51e73cc0] generated 2942474370 positions
2022-01-20 13:32:16 [2b9b51e73cc0] sorted 2942474370 positions
2022-01-20 13:32:16 [2b9b51e73cc0] STAT: AlignWorkflow::selectMatches 35312574464vm 7886759res
2022-01-20 13:32:16 [2b9b51e73cc0] Selecting matches using BinIndexMap(10000bl)
2022-01-20 13:32:16 [2b9b51e73cc0] STAT: before buildBinPathList 35312574464vm 7886786res
2022-01-20 13:32:18 [2b9b51e73cc0] found 1757 unique bin paths in 312770 binsError: 2022-Jan-20 13:32:21: Too many open files: /wynton/home/rotation/mtsui/ASE_project/Isaac4/src/c++/include/io/FileBufWithReopen.hh(56): Throw in function isaac::io::basic_FileBufWithReopen<_CharT, _Traits>::basic_FileBufWithReopen(const isaac::io::basic_FileBufWithReopen<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]
Dynamic exception type: boost::exception_detail::clone_impl<isaac::common::IoException>
std::exception::what: Failed to allocate a file handle
: Failed to allocate a file handle
Any suggestions would be appreciated, thanks!!
Maggie
isaac4 for mouse
Hi,
I successfully installed isaac4 in my linux server, and finished the mapping for human WGS samples quickly!
However, when I used isaac4 to map mouse WGS samples. It failed, the error is like this:
2018-01-26 06:17:49 [7f545486a700] ERROR: Thread: 12 caught an exception first: 2018-Jan-26 06:17:49: Success: /public1/users/xxw/software/isaa4/Isaac4-Isaac-04.17.06.15/src/c++/lib/build/Build.cpp(638): Throw in function bool isaac::build::Build::handleBinAllocationFailure(bool, const isaac::alignment::BinMetadata&, const ExceptionType&, const ExceptionDataT&) [with ExceptionType = std::bad_alloc; ExceptionDataT = long unsigned int]
Dynamic exception type: boost::exception_detail::clone_implisaac::common::ThreadingException
std::exception::what: ERROR: Failing due to: BinMetadata(29415id ReferencePosition(1:98660000:f)bs 10000bl 13051034234ds 0do 0se 19543367rs 19972219f /public1/users/xxw/isaac/,mouse/ABE_mouse/mDMD-2/./Temp/bin-00000002-094358955.dat) blocking everything with std::bad_alloc : std::bad_alloc Error data: 17317002114
: ERROR: Failing due to: BinMetadata(29415id ReferencePosition(1:98660000:f)bs 10000bl 13051034234ds 0do 0se 19543367rs 19972219f /public1/users/xxw/isaac/,mouse/ABE_mouse/mDMD-2/./Temp/bin-00000002-094358955.dat) blocking everything with std::bad_alloc : std::bad_alloc Error data: 17317002114
..........
: Terminating due to failures on other threads
2018-01-26 06:17:49 [7f553aaeb740] WARNING: rethrowing a thread exception
2018-01-26 06:17:49 [7f553aaeb740] md5 checksum for /public1/users/xxw/isaac/,mouse/ABE_mouse/mDMD-2/out_dir/Projects/default/default/sorted.bam:fb8ffdeeffb283b7cabad84b4296ce94
Error: 2018-Jan-26 06:17:49: Success: /public1/users/xxw/software/isaa4/Isaac4-Isaac-04.17.06.15/src/c++/lib/build/Build.cpp(638): Throw in function bool isaac::build::Build::handleBinAllocationFailure(bool, const isaac::alignment::BinMetadata&, const ExceptionType&, const ExceptionDataT&) [with ExceptionType = std::bad_alloc; ExceptionDataT = long unsigned int]
Dynamic exception type: boost::exception_detail::clone_implisaac::common::ThreadingException
std::exception::what: ERROR: Failing due to: BinMetadata(29415id ReferencePosition(1:98660000:f)bs 10000bl 13051034234ds 0do 0se 19543367rs 19972219f /public1/users/xxw/isaac/,mouse/ABE_mouse/mDMD-2/./Temp/bin-00000002-094358955.dat) blocking everything with std::bad_alloc : std::bad_alloc Error data: 17317002114
: ERROR: Failing due to: BinMetadata(29415id ReferencePosition(1:98660000:f)bs 10000bl 13051034234ds 0do 0se 19543367rs 19972219f /public1/users/xxw/isaac/,mouse/ABE_mouse/mDMD-2/./Temp/bin-00000002-094358955.dat) blocking everything with std::bad_alloc : std::bad_alloc Error data: 17317002114
Looking forward to your reply urgently!
Thanks very much from my heart!
xiaowei,
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.